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#1277 SMILES with bad stereochemistry is not parsed #2851

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#1277 SMILES with bad stereochemistry is not parsed

#1277 SMILES with bad stereochemistry is not parsed #2851

GitHub Actions / macos-x86_64-java_test_report failed Sep 15, 2023 in 0s

249 tests run, 243 passed, 0 skipped, 6 failed.

Annotations

Check failure on line 1 in api/c/tests/unit/tests/basic.cpp

See this annotation in the file changed.

@github-actions github-actions / macos-x86_64-java_test_report

basic.fold_unfold 

[FAILED]
Raw output 
Diff:
- C1([C@H](O)[C@H]([C@H](OC2C=CC([N+]([O-])=O)=CC=2)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O |&1:1,3,4,16,21,22,24,25,27,r|
+ C1([C@H](O)[C@H]([C@H](OC2C=CC([N+]([O-])=O)=CC=2)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O |&1:1,3,4,16,21,22,24,25,27,r,wU:0.0,wD:0.21|
- C1([H])([C@]([H])(O[H])[C@]([H])([C@]([H])(OC2C([H])=C([H])C([N+]([O-])=O)=C([H])C=2[H])O[C@]1([H])C([H])([H])O[H])O[H])O[C@]1([H])[C@]([H])(O[H])[C@]([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])O[H])O1)O[H] |&1:2,6,8,25,35,37,41,43,47,r|
+ C1([H])([C@]([H])(O[H])[C@]([H])([C@]([H])(OC2C([H])=C([H])C([N+]([O-])=O)=C([H])C=2[H])O[C@]1([H])C([H])([H])O[H])O[H])O[C@]1([H])[C@]([H])(O[H])[C@]([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])O[H])O1)O[H] |&1:2,6,8,25,35,37,41,43,47,r,wU:0.1,wD:0.35|
- C1([C@H](O)[C@H]([C@H](OC2C=CC([N+]([O-])=O)=CC=2)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O |&1:1,3,4,16,21,22,24,25,27,r|
+ C1([C@H](O)[C@H]([C@H](OC2C=CC([N+]([O-])=O)=CC=2)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O |&1:1,3,4,16,21,22,24,25,27,r,wU:0.0,wD:0.21|

Check failure on line 1 in api/c/tests/unit/tests/basic.cpp

See this annotation in the file changed.

@github-actions github-actions / macos-x86_64-java_test_report

basic.stereocenters 

[FAILED]
Raw output 
Diff:
- 261: C1([C@H](O)[C@H]([C@H](OC2C=CC([N+]([O-])=O)=CC=2)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O |&1:1,3,4,16,21,22,24,25,27,r|
+ 261: C1([C@H](O)[C@H]([C@H](OC2C=CC([N+]([O-])=O)=CC=2)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O |&1:1,3,4,16,21,22,24,25,27,r,wU:0.0,wD:0.21|

Check failure on line 1 in exact

See this annotation in the file changed.

@github-actions github-actions / macos-x86_64-java_test_report

exact.reload 

[ERROR]
Raw output 
Error:
Traceback (most recent call last):
  File "api/tests/integration/test.py", line 356, in run_test_module
    runpy.run_path(module_filename, run_name="__main__")
  File "/Users/runner/work/Indigo/Indigo/jython.jar/Lib/runpy$py.class", line 240, in run_path
    return _run_module_code(code, init_globals, run_name, path_name)
  File "/Users/runner/work/Indigo/Indigo/jython.jar/Lib/runpy$py.class", line 81, in _run_module_code
    _run_code(code, mod_globals, init_globals,
  File "/Users/runner/work/Indigo/Indigo/jython.jar/Lib/runpy$py.class", line 72, in _run_code
    exec code in run_globals
  File "/Users/runner/work/Indigo/Indigo/api/tests/integration/tests/exact/reload.py", line 59, in <module>
    testMol(item)
  File "/Users/runner/work/Indigo/Indigo/api/tests/integration/tests/exact/reload.py", line 59, in <module>
    testMol(item)
  File "/Users/runner/work/Indigo/Indigo/api/tests/integration/tests/exact/reload.py", line 43, in testMol
    msg = (
TypeError: not enough arguments for format string

Check failure on line 1 in api/c/tests/unit/tests/inchi.cpp

See this annotation in the file changed.

@github-actions github-actions / macos-x86_64-java_test_report

inchi.compare 

[FAILED]
Raw output 
Diff:
-   Smiles1: O[C@@H]1[C@@]2([H])C(N[C@@H]([C@@H](C[C@@H](C(N[C@@]([H])([C@@H](C)O)C(N3C[C@@H](CC3([H])C(N[C@@]([H])([C@@H]([C@H](C3C=CC(=CC=3)O)O)O)C(N[C@@]([H])([C@@H](C)O)C(N2C[C@@H]1C)=O)=O)=O)O)=O)=O)NC(C1C=CC(C2C=CC(C3C=CC(=CC=3)OCCCCC)=CC=2)=CC=1)=O)O)O)=O
+   Smiles1: O[C@@H]1[C@@]2([H])C(N[C@@H]([C@@H](C[C@@H](C(N[C@@]([H])([C@@H](C)O)C(N3C[C@@H](CC3([H])C(N[C@@]([H])([C@@H]([C@H](C3C=CC(=CC=3)O)O)O)C(N[C@@]([H])([C@@H](C)O)C(N2C[C@@H]1C)=O)=O)=O)O)=O)=O)NC(C1C=CC(C2C=CC(C3C=CC(=CC=3)OCCCCC)=CC=2)=CC=1)=O)O)O)=O |wD:22.23|

Check failure on line 1 in api/tests/integration/ref/rpe/rpe.py.out

See this annotation in the file changed.

@github-actions github-actions / macos-x86_64-java_test_report

rpe.transform_basic 

[FAILED]
Raw output 
Diff:
- Br.CC(N1([C@@H]2CC[C@H]1C[C@@H](OC(C(C1=CC=CC=C1)CO)=O)C2)C)C
+ Br.CC(N1([C@@H]2CC[C@H]1C[C@@H](OC(C(C1=CC=CC=C1)CO)=O)C2)C)C |wU:3.24|
- Br.CC(N1([C@@H]2CC[C@H]1C[C@@H](OC(C(C1=CC=CC=C1)CO)=O)C2)C)C
+ Br.CC(N1([C@@H]2CC[C@H]1C[C@@H](OC(C(C1=CC=CC=C1)CO)=O)C2)C)C |wU:3.24|

Check failure on line 1 in api/tests/integration/tests/basic/molecules/stereo.mol

See this annotation in the file changed.

@github-actions github-actions / macos-x86_64-java_test_report

stereo.bidirectional 

[FAILED]
Raw output 
Diff:
- 07.mol C1CCC(C2C=CC(N([H])C2=O)=O)O1
+ 07.mol C1CCC(C2C=CC(N([H])C2=O)=O)O1 |wU:3.2,wD:3.3|
- 10.mol C1CCC(C)(C2C=CC(N([H])C2=O)=O)O1
+ 10.mol C1CCC(C)(C2C=CC(N([H])C2=O)=O)O1 |wD:3.3,3.4|
- 16.mol C1CC[C@@](C)(C2(C)C=CC(N([H])C2=O)=O)O1 |&1:3,r|
+ 16.mol C1CC[C@@](C)(C2(C)C=CC(N([H])C2=O)=O)O1 |&1:3,r,wU:5.4,5.5|
- 17.mol C1CCC(C)([C@]2(C)C=CC(N([H])C2=O)=O)O1 |&1:5,r|
+ 17.mol C1CCC(C)([C@]2(C)C=CC(N([H])C2=O)=O)O1 |&1:5,r,wU:3.3,3.4|
- test.mol C(C)(O)N
+ test.mol C(C)(O)N |wU:0.1,wD:0.2|
- test2.mol C1(CCCO1)N
+ test2.mol C1(CCCO1)N |wU:0.4,wD:0.5|
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